How to prevent CP 3000+ pokemons from losing motivation unreasonably quickly?
No, this is not a bug and the way to prevent is well - feed it berries. Higher CP Pokémon, by design, lose motivation faster than lower CP Pokémon
This article states
First of all, it’s important to note that Pokemon lose motivation gradually over time, even if they are not defeated in battle. The exact formula depends on the Pokemon, but Pokemon with higher CPs lose motivation quicker than Pokemon with lower CPs. This is something that has been confirmed by Niantic.
“To help balance different Pokémon strengths and abilities, stronger Pokémon generally lose motivation more quickly than those that are not as strong,” Niantic said on its website.
Niantic Support
To help balance different Pokémon strengths and abilities, stronger Pokémon generally lose motivation more quickly than those that are not as strong.